Maybe as a quick work around, have the first timeline set to Start on Layout 1 by default?
The problem is timelines aren't actually associated with a layout - they are essentially global and can be used on any layout, and so there also isn't really a good "default layout" to play them on, according to the current design. The default for the first timeline could be changed, but then the first timeline works differently to any timelines you add next. In my experience that just moves the stumbling block for beginners - the question just moves from "why doesn't my first timeline play?" to "why doesn't my second timeline play?". Even if you have to figure out how to play the first timeline, at least you've learned the principle and can apply that to any timeline, instead of relying on defaults you haven't found out about yet.
I agree that it would be nice to have a smoother experience for first-time visitors, but I'm not sure how to best solve this without introducing a new inconsistency.
Maybe have it use the framerate from the first timeline?
We don't yet have a property named 'framerate' for timelines... do you mean what we currently call 'Steps per second'?
Maybe an export option for making the bottom layer background transparent then?
Well, what is the bottom layer? That is a surprisingly difficult question. What if the bottom layer has sub-layers? Maybe it's the last sub-layer? But that is drawn after the root bottom layer, and could well be transparent anyway. What about the root bottom layer? That could actually be transparent and only used for a compositing effect, and in fact a sub-layer has the opaque background. There could be multiple sub-layers with opaque backgrounds, some used for fade effects, and only one truly being the background.
I don't think there is actually a good way to automatically identify "the background layer", so I don't think we can make a reliable setting for it, hence the advice in the dialog instead - presumably the project author knows!